Context: Research into improving feed efficiency by ruminant animals grazing pastures has historically been restrained by an inability to measure feed intake by large numbers of individual animals. Recent advances in portable breath measurement technology could be useful for this purpose but methodologies need to be developed.

Aims: To evaluate predictive models for metabolisable energy intake (MEI) by free-ranging cattle using multiple short-term breath samples and then apply these to predict MEI by free-ranging cattle in a historic grazing experiment with cattle genetically divergent for residual feed intake (feed efficiency).

Methods: Predictive models for MEI were developed using bodyweight (BW) data, and carbon dioxide production rate (CPR) and methane production rate (MPR) from multiple short-term breath measurements, from an experiment with long-fed Angus steers on a grain-based diet, and an experiment with short-fed Angus heifers on a roughage diet. Heat production was calculated using CPR and MPR. Energy retained (ER) in body tissue gain by steers was calculated from BW, ADG, initial and final subcutaneous fat depths, and for both groups using feeding-standards equations.

Key results: Metabolic mid-test BW (MBW) explained 49 and 47% of the variation in MEI in the steer and heifer experiment, respectively, and for the steers adding ADG and then subcutaneous fat gain resulted in the models accounting for 60 and then 65% of the variation in MEI. In the steer experiment, MBW with CPR explained 57% of the variation in MEI, and including MPR did not account for any additional variation. In the heifer experiment, MBW with CPR explained 50%, and with MPR accounted for 52% of the variation in MEI. Heat production plus ER explained 60, 35 and 85% of the variation in MEI in the steer and the heifer experiments, and in the pooled data from both experiments, respectively.

Conclusions: Multiple short-term breath measurements, together simple BW data, can be used to predict MEI by free-ranging cattle in studies in which animals do not have feed-intake or ADG recorded.

Implications: This methodology can be used for research into improving feed efficiency by farm animals grazing pastures.

Establishment ofthe rumen microbiome can be affected by both early-life dietary measures and rumen microbial inoculation. This study used a 2 × 3 factorial design to evaluate the effects of inclusion of dietary fat type and the effects of rumen inoculum from different sources on ruminal bacterial communities present in early stages of the lambs' life. Two different diets were fed ad libitum to 36 pregnant ewes (and their lambs) from 1 month prelambing until weaning. Diets consisted of chaffed lucerne and cereal hay and 4% molasses, with either 4% distilled coconut oil (CO) provided as a source of rumen-active fat or 4% Megalac® provided as a source of rumen-protected fat (PF). One of three inoculums was introduced orally to all lambs, being either (1) rumen fluid from donor ewes fed the PF diet" (2) rumen fluid from donor ewes fed CO" or (3) a control treatment of MilliQ-water. After weaning at 3 months of age, each of the six lamb treatment groups were grazed in spatially separated paddocks. Rumen bacterial populations of ewes and lambs were characterised using 454 amplicon pyrosequencing of the V3/V4 regions of the 16S rRNA gene. Species richness and biodiversity of the bacterial communities were found to be affected by the diet in ewes and lambs and by inoculation treatment of the lambs. Principal coordinate analysis and analysis of similarity (ANOSIM) showed between diet differences in bacterial community groups existed in ewes and differential bacterial clusters occurred in lambs due to both diet and neonatal inoculation. Diet and rumen inoculation acted together to clearly differentiate the bacterial communities through to weaning, however the microbiome effects of these initial early life interventions diminished with time so that rumen bacterial communities showed greater similarity 2 months after weaning. These results demonstrate that ruminal bacterial communities of newborn lambs can be altered by modifying the diet of their mothers. Moreover, the rumen microbiome of lambs can be changed by diet while they are suckling or by inoculating their rumen, and resulting changes in the rumen bacterial microbiome can persist beyond weaning.

Demand for livestock products and methane mitigation is increasingly stimulating a search for technologies capable of increasing animal productivity while lowering enteric methane emissions. Dietary nitrate (NO₃⁻) has shown this capability in sheep on low nitrogen diets. Cysteamine hydrochloride (CSH) has also been shown to have such dual efficacy, but whether it affects rumen fermentation directly or indirectly by modifying digesta kinetics is unknown. It was hypothesized that the administration of CSH to cattle would reduce in-vitro and in-vivo methane production and also increase their average daily liveweight gain (LWG) without affecting their DM intake (DMI). An in-vitro experiment was conducted to study the effects of CSH, NO₃⁻, urea and nitrite, on methane and volatile fatty acid (VFA) production and on the protozoal population. Methane production, production of total VFA and acetate, and acetate:propionate ratio were not affected by CSH (P > 0.05) relative to control incubations, however, pH was reduced while hydrogen accumulation was increased (P < 0.05) by CSH relative to control incubations. Subsequently, a 42-d in-vivo experiment was conducted using a completely randomized design with twelve yearling cattle (236 ± 49 kg liveweight; LW) to assess LWG, methane production and feed conversion ratio (FCR) on a basal roughage/concentrate diet containing either no additives, or 1% NO₃⁻ addition, or 80 mg/kg LW of CSH. Daily methane production rate (DMP; g methane/d) was measured over 2 × 24 h periods in open-circuit calorimetry chambers during both weeks 3 and 6 of the study, with nutrient digestibility determined by collecting faecal samples and using acid insoluble ash as an indigestible marker. Relative to cattle fed the control diet CSH supplemented cattle exhibited no change in LWG or FCR (P > 0.05). While neither DMP nor methane yield (MY; methane/kg DMI) were reduced by CSH (mean 9.2% reduction), methane production rate was significantly reduced (P < 0.05.) for up to 6 h post-feeding relative to control animals. Nitrate reduced MY by 31.1% (15.7 g methane/kg DMI; P < 0.01) relative to when the control diet was fed (22.8 g methane/kg DMI), and increased (P < 0.01) dietary crude protein digestibility. It was concluded that while NO₃⁻ can deliver greater methane mitigation than CSH, CSH has in some studies (though not this study) improved the efficiency of animal production, which, together with the observed short term efficacy in reducing methane emissions suggests CSH may have a role in enabling greater animal production at a reduced environmental cost.

Effects of rumen protozoa on ruminal fermentation, methane (CH4) emissions and nitrogen (N) retention were studied in twelve crossbred ewes given an oaten chaff diet. Over 10 days sheep were progressively adapted to a diet containing 7% coconut oil distillate to suppress rumen protozoa and then were defaunated using sodium 1-(2-sulfonatooxyethoxy) dodecane (Empicol). Twelve weeks after defaunation treatment, five sheep were inoculated with rumen fluid collected from cannulated sheep to refaunate them and that the effect of re-establishment of rumen protozoa 0, 7, 14 and 21 days following refaunation on ruminal fermentation and CH4 emissions was examined in Experiment 1. As a following study (Experiment 2), feed intake was restricted to 1.5 x ME requirement for maintenance from day 28 to day 43 when dry matter (DM) digestibility, N retention, fermentation and CH4 emissions were compared between defaunated and refaunated sheep. Sheep were scanned through a computed tomography scanner on day 0 and day 28 to estimate reticulo-rumen (RR) weight and carcass composition. It was concluded that refaunated sheep did not have a higher daily CH4 production (DMP, g CH4/day) than did the defaunated cohort within 21 days after refaunation as measured by Greenfeed Emission Monitoring units. Total volatile fatty acid (VFA) concentration and the proportion of propionate in the rumen VFA gradually increased over 21 days following refaunation (Experiment 1), while a change towards higher butyrate and lower acetate proportions was observed after 28 days (Experiment 2; P<0.05). There was a tendency towards a heavier RR weight (P=0.08) and a higher ratio of RR to liveweight in defaunated sheep 28 days after refaunation (P < 0.001), but carcass composition was not affected by refaunation status. Experiment 2 showed defaunated sheep had a 7% lower DMP than did refaunated sheep with an established rumen fauna (P<0.05). Apparent whole-tract N and DM digestibility and microbial crude protein supply were not different between defaunated and refaunated sheep, while energy losses in CH4 (MJ/day) and CH4 as a proportion of gross energy intake were both approximately 8% lower in defaunated sheep. The reduced CH4 emissions achieved by defaunation occurred without altering total VFA, apparent whole-tract N and DM digestibility or ADG.

Divergent genetic selection for wool growth as a single trait has led to major changes in sheep physiology and metabolism, including variations in rumen microbial protein production and uptake of α-amino nitrogen in portal blood. This study was conducted to determine if sheep with different genetic merit for wool growth exhibit distinct rumen bacterial diversity. Eighteen Merino wethers were separated into groups of contrasting genetic merit for clean fleece weight (CFW; low: WG- and high: WG+) and fed a blend of oaten and lucerne chaff diet at two levels of intake (LOI; 1 or 1.5 times maintenance energy requirements) for two seven-week periods in a crossover design. Bacterial diversity in rumen fluid collected by esophageal intubation was characterized using 454 amplicon pyrosequencing of the V3/V4 regions of the 16S rRNA gene. Bacterial diversity estimated by Phylogenetic distance, Chao1 and observed species did not differ significantly with CFW or LOI; however, the Shannon diversity index differed (P=0.04) between WG+ (7.67) and WG- sheep (8.02). WG+ animals had a higher (P=0.03) proportion of Bacteroidetes (71.9% vs 66.5%) and a lower (P=0.04) proportion of Firmicutes (26.6% vs 31.6%) than WG+ animals. Twenty-four specific operational taxonomic units (OTUs), belonging to the Firmicutes and Bacteroidetes phyla, were shared among all the samples, whereas specific OTUs varied significantly in presence/abundance (P<0.05) between wool genotypes and 50 varied (P<0.05) with LOI. It appears that genetic selection for fleece weight is associated with differences in rumen bacterial diversity that persist across different feeding levels. Moderate correlations between seven continuous traits, such as methane production or microbial protein production, and the presence and abundance of 17 OTUs were found, indicating scope for targeted modification of the microbiome to improve the energetic efficiency of rumen microbial synthesis and reduce the greenhouse gas footprint of ruminants.

The hypothesis tested by this study was that sheep with divergent estimated breeding values (EBV) for fleece weight differ in gut metabolism and anatomy" regardless of the level of intake. Adult Merino wethers with contrasting EBVs for fleece weight were fed at two levels of intake in two 7-week periods in a crossover design, where wool growth, gut metabolism and anatomy of the sheep were evaluated. Regardless of the level of intake, wool genotype affected wool growth (P<0.05); however, rumen metabolism and gut anatomy did not differ between wool genotypes (P<0.05). Increases in the level of intake increased the supply of nutrients to the animal and the measured end-products of the process (wool production, live weight, methane) independent of wool genotype. The results obtained in this study indicate that differences in gut fermentation and anatomy are not a major cause of differences in wool production among sheep of different estimated genetic merit for fleece weight when fed restricted intakes.

A 2 x 2 factorial experiment was conducted to assess the effects of presence or absence of rumen protozoa and of dietary coconut oil distillate (COD) supplementation on rumen fermentation characteristics, digesta kinetics and methane production in Brahman heifers. Twelve Brahman heifers were selected to defaunate, with 6 being subsequently refaunated. After defaunation and refaunation, heifers were randomly allocated to COD supplement or no supplement treatments while fed an oaten chaff-based diet. Methane production (MP; 94.17 v 104.72 g CH₄/d) and methane yield [MY; 19.45 v 21.64 g CH₄/kg dry matter intake (DMI)] were reduced in defaunated heifers compared with refaunated heifers when measured at 5 weeks after refaunation treatment (p < 0.01). Supplement of COD similarly reduced MP and MY (89.36 v 109.53 g/d and 18.46 v 22.63 g/kg DMI, respectively; p < 0.01), and there were no significant interactions of defaunation and COD effects on rumen fermentation or methane emissions. Concentration of total volatile fatty acid (VFA) and molar proportions of acetate, propionate and butyrate was not affected by defaunation or by COD. Microbial crude protein (MCP; g/d) outflow was increased by defaunation (p < 0.01) in the absence of COD but was unaffected by defaunation in COD-supplemented heifers. There was a tendency towards a greater average daily gain (ADG) in defaunated heifers (p = 0.09), but COD did not increase ADG (p > 0.05). The results confirmed that defaunation and COD independently reduced enteric MP even though the reduced emissions were achieved without altering rumen fermentation VFA levels or gut digesta kinetics.